開發冗餘分析應用系統

基因不只是一個具有功能性的遺傳基本單位，還與人類的疾病息息相關，目前基因研究已成為最熱門的話題之一。幾乎每個生物體都擁有基因，它由DNA或RNA 序列所組成，透過知道基因產物的合成，如RNA或蛋白質，來表達它所攜帶的遺傳訊息，目前已被測定的核苷酸序列都被儲存於一個大資料庫，如GenBank。為了確保生物體裡的基因正確無誤地表達，基因也如自動控制系統般擁有備份，所以有些生化功能可以由超過一組的基因來表達，這些复本被稱為基因冗餘。基因冗餘也廣泛存在於病原菌之中，並且與細菌的抗藥性有關。細菌擁有快速的繁衍速度所以能在進化能力較強，使用錯誤的抗生素或劑量不足，都可讓生還的細菌產生突變，進而擁有抗藥性使其繼續生存。在這項研究裡，設想這些有關於細菌生存的重要基因，為防出錯而擁有基因冗餘，因此辨別這些基因有助於開發對抗病原菌的藥物或對策。目前有許多核酸序列資料庫已經被開發，卻很難找到針對基因冗餘的資料庫，因此這項研究針對使用者的目的，收集擁有冗餘的相關基因以讓辨別這些基因的時間縮短，為此建設了與病原體抗藥性有關的基因冗餘資料庫以作為例子。另一方面，此研究設計了一個應用系統，擁有使用者介面及與所開發的資料庫相連，因此使用者可以將想查看的基因序列輸入系統以作比對。在應用系統設計及開發後，續而測試其使用性能及準確率。當此系統開始時，將出現一個選單以讓使用者選擇所要輸入的基因序列種類，共有三項選擇: 1)氨基酸序列；2) DNA序列；3)RNA序列。為防止使用者輸入錯誤的字元造成系統錯誤而停止運作，若使用者輸入不屬於該基因序列的資源，將會出現訊息告知，以讓使用者重新檢視其基因序列。最後，此研究使用了2組基因樣本以作測試，測試結果不知可顯示做找到的基因名字及其數量，也會統計所發現的基因家族種類及數量。細菌是個快速生長的生物體，因此在月短的時間內找到應對方案可以預防細菌擴散，減少對人類的危害。依據現有的研究發現，導致抗藥性的基因有一部分擁有冗餘的存在，但這些基因資訊被存放在一個擁有各種生物體基因資訊的資料庫，造成對時將十分耗時。所以針對使用需求，發一個資訊較有針對性及精簡的資料庫，將有助於縮短比對基因樣本的時間及減輕應用系統的負擔，而且此系統也可沿用到任何擁有基因的生物體，如病毒。未來也可結合基因定序及此應用系統，開發一個可攜帶的裝置，以便在實驗室外也可進行檢測及給予相應的方案。

關鍵字

基因冗餘；基因定序；氨基酸序列； DNA序列； RNA序列

並列摘要

Genetic research is an important topic to discuss nowadays, it is not only a basic physical and functional unit of heredity, but it also highly related to some human diseases. Gene exists in almost every living organism, it gives the instruction to synthesize the genetic product, like RNA or protein. Gene is made up of DNA or RNA sequences, the genetic sequence that has been discovered are stored in databases, like GenBank. To assure the organism to function well or alive, some biochemical function can bring out by more than a gene like a backup mechanism, these genes are called redundant genes. Genetic redundancy is also widely existed in many pathogenic bacteria, one of the known function that redundant gene leads to is drug resistance, the bacterial reproduction is at a fast rate so bacteria can evolve quickly, an insufficient dose or incorrect antibiotics might give them a chance to mutant into a more dominant species. This study assumes that the genes which are crucial with their survival will have a redundancy, identical those redundant genes will help in designing a treatment to treat the pathogenic bacteria which threaten human health. Many genetic databases have been developed recently but it is hard to find a database is specialize for genetic redundancy. This study gives an idea that databases of redundant genes can be developed based on the purpose of usage so it can shorten the time of sorting out the redundant gene, and a database of redundant genes related to the drug resistance can be found in the pathogenic bacteria has developed as an example. On the other hand, another user interface will be designed to connect with the database, so the user can insert and compare the genetic sequence of the sample gene with the information of redundant genes in the database. The application has been developed and tested its efficiency, a menu allows users to choose the genetic sequences that would like to input when the application started, there has three options: 1) Amino Acid Sequence; 2) DNA sequence; 3) RNA sequence. To avoid the errors stop the system from running, if the user inputted any wrong characters which do not belong to the genetic sequence, an error message will be outputted. Two sample genes have been inputted separately to check for the accuracy of the system, the result shows that the application can show the name of the found gene and its quantity, continue by the total gene number of the founded gene family. Bacteria have a fast reproduction rate, finding a treatment in a short time can prevent the spreading of pathogenic bacteria. Recent researches show that some of the genes which cause drug resistance are redundant genes, and those genetic information are stored in a big database which included various type of organism or species, so it is time-consuming to identify the redundant genes. Therefore, a database created for special usage can simplify the data and only related information is included, so the time of identifying a sample gene will be shortened and the burden of the system will be decreased. Besides, this application is not only limited to bacteria, it can be widely used by any organism with genetic sequences, like viruses. In the future, a portable device can be designed to combine both gene sequencing and identify gene redundancy, so it will be more convenient to check the raw data outdoor and design treatment.

並列關鍵字

genetic redundancy ； genome sequence ； amino acid sequence ； DNA sequence ； RNA sequence

參考文獻

1. Carrasco-Hernandez, R., Jácome, R., López Vidal, Y., Ponce de León, S. (2017). Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review. ILAR journal, 58(3), 343–358. https://doi.org/10.1093/ilar/ilx026

Google Scholar

2. Connie Rye, Robert Wise, Vladimir Jurukovski, Jean DeSaix, Jung Choi, Yael Avissar (2016). Biology, OpenStax

Google Scholar

3. Chial, H. (2008) DNA sequencing technologies key to the Human Genome Project. Nature Education 1(1):219

Google Scholar

4. Ascencio D., DeLuna A. (2013). Genetic Redundancy. In: Dubitzky W., Wolkenhauer O., Cho KH., Yokota H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY., https://doi.org/10.1007/978-1-4419-9863-7_1167

Google Scholar

5. Hurles M (2004), Gene Duplication: The Genomic Trade in Spare Parts, PLoS Biol 2(7): e206. https://doi.org/10.1371/journal.pbio.0020206

Google Scholar

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開發冗餘分析應用系統

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